The STEM Model Generator supports developers who want to create a new disease or population model in STEM rather than use an existing model. Setting up the basic structure for a new model can be challenging. This tutorial provides step-by-step instructions for using the STEM Model Generator to design and generate the structure of a new STEM computational (disease/population) model project.

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Note: This feature is currently intended for use in the Eclipse SDK only.

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=== Acknowledgements ===

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The development of the Model Generator tool was sponsored in part by the [http://www.bfr.bund.de German Federal Institute for Risk Assessment (BfR)]. Additional special thanks to Alex Falenski from BfR for assistance creating and editing this document.

'''Important note''':&nbsp; the STEM Model Generator is currently intended for use in the Eclipse SDK only.&nbsp; '''''It is not intended for installation or use within the STEM application.'''''

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'''Important note''':&nbsp; The STEM Model Generator is currently intended for use in the Eclipse SDK only.&nbsp; '''''It is not intended for installation or use within the STEM application.'''''

== Generate a STEM Computational Model Project ==

== Generate a STEM Computational Model Project ==

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=== Add/Edit a Computational Model ===

=== Add/Edit a Computational Model ===

When you're ready to add a computational model to the package, from the '''Model Package''' page, click '''Add Model'''. To edit an existing computational model, select it in the '''Contained Models''' list and click '''Edit Model'''.

When you're ready to add a computational model to the package, from the '''Model Package''' page, click '''Add Model'''. To edit an existing computational model, select it in the '''Contained Models''' list and click '''Edit Model'''.

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This will launch the Computational Model Wizard.

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This will launch the '''Computational Model Wizard'''.

==== Configure Model Properties ====

==== Configure Model Properties ====

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:[[Image:STEM-ModelGen-ParamsPage.png|500px]]

:[[Image:STEM-ModelGen-ParamsPage.png|500px]]

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By default, a model inherits parameters from its ancestor models. These are show in <span style="color: #a0a0a0; font-style:italic;">light gray italics</span>. '''You cannot edit or remove parameters inherited from another model.'''

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By default, a model inherits parameters from its ancestor models. These are shown in <span style="color: #a0a0a0; font-style:italic;">light gray italics</span>. '''You cannot edit or remove parameters inherited from another model.'''

To add a new model parameter, click '''Add Parameter'''. To edit an existing parameter, select one from the list and click '''Edit Parameter'''.

To add a new model parameter, click '''Add Parameter'''. To edit an existing parameter, select one from the list and click '''Edit Parameter'''.

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When you click '''Add''' or '''Edit Parameter''', the '''Model Parameter Editor''' window opens. Use the form provided to set the properties for the model parameter.

When you click '''Add''' or '''Edit Parameter''', the '''Model Parameter Editor''' window opens. Use the form provided to set the properties for the model parameter.

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| '''Property '''

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:[[Image:STEM-ModelGen-CompartmentDialog-Standard.png]]

:[[Image:STEM-ModelGen-CompartmentDialog-Standard.png]]

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#: [[Image:STEM-ModelGen-PkgExplorer-DiseaseModel.png]]

#: [[Image:STEM-ModelGen-PkgExplorer-DiseaseModel.png]]

# Double click on your computational model's Java class. This is named '''[YourModelName]Impl.java'''.

# Double click on your computational model's Java class. This is named '''[YourModelName]Impl.java'''.

About

The STEM Model Generator supports developers who want to create a new disease or population model in STEM rather than use an existing model. Setting up the basic structure for a new model can be challenging. This tutorial provides step-by-step instructions for using the STEM Model Generator to design and generate the structure of a new STEM computational (disease/population) model project.

Note: This feature is currently intended for use in the Eclipse SDK only.

Installation

Important note: The STEM Model Generator is currently intended for use in the Eclipse SDK only. It is not intended for installation or use within the STEM application.

Generate a STEM Computational Model Project

Launch the STEM Model Generator Wizard

Open the Eclipse SDK

Open the File menu, New, and choose Other

You can also do Control-N (Command-N on Mac OS X)

In the list of Wizards, expand the STEM category and select New STEM Model Project

Click Next

Choose Create and configure a new STEM Model Package

Click Next

Configure the Model Package

The model package is the container for all models in a given package. A model package generates an Eclipse plug-in project.

Parameter Name

Data Type

Example Value

Package Name

String(Java Identifier)

CattleSalmonellosis

Package Prefix

String(Java Package Identifier)

com.example.diseasemodels

The Package Name and Package Prefix are combined to create the resulting Eclipse plug-in/project identifier. For example, the model package with values above will generate an Eclipse plug-in/project with ID com.example.diseasemodels.cattlesalmonellosis.

Add/Edit a Computational Model

When you're ready to add a computational model to the package, from the Model Package page, click Add Model. To edit an existing computational model, select it in the Contained Models list and click Edit Model.
This will launch the Computational Model Wizard.

Configure Model Properties

Model properties are the most basic settings of a STEM Computational Model. Properties include the model's name, the model's type, and which parent model it extends and inherits parameters and compartments from. All are required.

Property

Type

Example

Description

Model Name

String(Java Identifier)

CattleSalmonella

The model's name. This value will be the Java class name of the generated model. Should contain alphanumeric characters, no spaces, and cannot begin with a number.

Model Type

String from list

DiseaseModel

The underlying model type. If you're implementing a Disease Model, select DiseaseModel. A Population Model, select PopulationModel. This value is used to find appropriate parent models.

Parent model

Computational Model

SIR

The computational model this new model will extend. If you're not sure, select the textbook model that most closely resembles the compartment model you're implementing (SI, SIR, SEIR)

When you're finished, click Next to configure the Model Parameters

Configure Model Parameters

Model parameters - also called rate parameters - represent user-defined variables that are passed into the computational model. The values can represent many things, but are often variables to the differential equations that make up the model. Users are asked to provide values for these parameters when a new Disease/Population/etc is created in STEM. Examples include Transmission Rate, Immunity Loss Rate, etc.

By default, a model inherits parameters from its ancestor models. These are shown in light gray italics. You cannot edit or remove parameters inherited from another model.

To add a new model parameter, click Add Parameter. To edit an existing parameter, select one from the list and click Edit Parameter.

When you click Add or Edit Parameter, the Model Parameter Editor window opens. Use the form provided to set the properties for the model parameter.

Property

Required?

Type

Example

Description

Name

Yes

String (Java Identifier)

transmissionRate2

The parameter's name. This is the name of the Java member variable in the resulting computational model. This required property is a Java identifier and should contain alphanumeric characters, no spaces, and cannot begin with a number.

Display Name

Yes

String

Transmission Rate 2

The display name of the parameter. This should be a short, user-friendly description of the parameter.

Data Type

Yes

EClassifier

double

The data type of the parameter. This will be the Java type of the resulting member variable. Tip: For models with multiple populations, select a ValueList or ValueMatrix data type.

Default Value

Yes**

Type-specific

0.0

The default value of the parameter if a value is not provided by the user. A default value often accompanies the parameter in literature. **This field is required for numeric data types (like double, integer, float, etc).

Constraints

No

Constraint

minValue

Parameter constraints are used to restrict the allowed parameter values. See below for more details about Parameter Constraints.

Units

No

String

PM/TP

User interface message that explains what units are expected for this parameter

Help Message

No

String

User interface message that further explains the purpose or other details about this parameter.

Missing Message

No

String

User interface message that displays when no value is entered for this parameter.

Invalid Message

No

String

User interface message that displays when an invalid value (e.g. violates the constraints) is entered for this parameter.

Parameter Constraints

Parameter constraints are used to restrict the allowed values for a model parameter. A parameter can have multiple constraints. Each constraint is evaluated independently and must be fulfilled for a value to be accepted.

Note: You can add multiple constraints of the same type. However, for certain constraint types, this may not make sense and may cause a value to never be valid. For example, it does not make sense to create two minValue constraints.

To add a new constraint, click Add . To edit an existing constraint, select one from the constraint list and click Edit.

Use the Constraint Editor to select the Constraint Type and enter a Constraint Value. When finished, click OK.

Available Constraints

Constraint Type

Example Constraint Value

Description

minValue

0.0

The minimum numeric value allowed for the parameter

maxValue

1.0

The maximum numeric value allowed for the parameter

More constraint types coming soon...

When you're finished working with Model Parameters, click Next to configure Model Compartments.

Configure Model Compartments

Model compartments are the second type of variable in the computational model and represent the various groupings within the model lifecycle. Unlike Model Parameters, however, these values are not defined by the user, but instead are calculated as the output from the model's differential equations. For more information, please read the Introduction to Compartment Models.

Like Model Parameters, Model Compartments are inherited from the parent model. Compartments inherited from another model are shown in light gray italics and cannot be edited or removed. If the compartments from your parent model do not closely match the compartment model you're implementing, you can elect to choose a different model to inherit compartments from.

Note: Just because a compartment does not match the compartment name in literature does not mean it's not logically the same or can't be reused. Consider this before deciding not to use an inherited compartment.

To add a new compartment, click Add Compartment. To edit an existing compartment, select it from the list and click Edit Compartment.

Use the Compartment Editor dialog to edit the compartment's properties. All properties are required.. When finished editing the compartment, click OK.

Property

Type

Example

Description

Compartment Name

String (Java identifier)

s

The name of the compartment. This is also the name of the resulting Java member variable. It should contain alphanumeric characters, no spaces, and cannot begin with a number.

Compartment Type

String

Standard

The property of values stored in the compartment. This helps determine what kinds of underlying calculations occur. Example types are Standard, Incidence, and Deaths.

Data Type

EClassifier

double

The data type of the compartment. Currently only valid type is double.

When you're finished working with compartments, the model is complete. Click Finish.

Run the Code Generator

When you're finished working with the computational models in the model package, you're ready to run the code generator.

From the Model Package page, click Next.

On the Generator Options, configure advanced properties for the code generator.

Advanced Generator Options coming soon!

When finished, click Finish.

If no errors are found, the code generator will now run. This process may take 1-2 minutes.

Work with your Generated Computational Models

Once the code generator finishes, the new computational model project will be imported into your Eclipse Workspace. You can now implement the model's mathematics directly into the new Java classes.

The new project is named after your Package Name and Package Prefix. For example, if you entered CattleSalmonellosis for the name and com.example.diseasemodels as the prefix, the resulting Eclipse project will be com.example.diseasemodels.cattlesalmonellosis.

In Eclipse's Package Explorer, find your new project and expand it

Under your project, expand the src tree

This will list several items that are named [YourProjectName].something.

Expand [YourProjectName].impl tree

Double click on your computational model's Java class. This is named [YourModelName]Impl.java.

Note: Double check to be sure you didn't select the LabelImpl/LabelValueImpl.java

In the Java file editor, scroll down to the calculateDeltas(...) method

Implement Scientific Logic!

See here for more help

Save

Load and Run Your Computational Model in STEM

Add Your New Model Project to STEM's Run Configuration

When you're ready to run and test your computational model in STEM, you must first tell Eclipse to include it in STEM's launch profile.

Notes About Editing an Existing Computational Model Project

The Model Generator is not intended for use on existing Disease/Population model projects that were previously created by hand. Please do not try running the Model Generator on projects that it did not originally create. You will almost certainly have to revert to what's in SVN.

Renaming/removing models, parameters, and compartments may cause compiler errors that will need to be fixed manually

If you change the name of an existing model, then a new model file will be created. Any code you implemented must be copied manually.

If you change the Package Name or Package Prefix, then a new model project will be created. Any code you implemented must be copied manually.

Use an existing EMF Ecore/GenModel with the Model Generator

It's possible to use the STEM Model Generator without using the Model Generator Wizard by EAnnotating to your EMF Ecore and applying the correct settings to your EMF GenModel. See here for instructions.